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An Optimised Faecal microRNA Sequencing Pipeline Reveals Fibrosis in Trichuris muris Infection

ABSTRACT: An Optimised Faecal microRNA Sequencing Pipeline Reveals Fibrosis in Trichuris muris Infection

PROVIDER: PRJNA1111849 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29040656.fastq.gz	Fastqsanger.gz
	SRR29040657.fastq.gz	Fastqsanger.gz
	SRR29040658.fastq.gz	Fastqsanger.gz
	SRR29040659.fastq.gz	Fastqsanger.gz
	SRR29040660.fastq.gz	Fastqsanger.gz

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An Optimised Faecal microRNA Sequencing Pipeline Reveals Fibrosis in Trichuris muris Infection

Project description:The intestine is a site of diverse functions including digestion, nutrient absorption, immune surveillance, and microbial symbiosis. As such, intestinal homeostasis is vital for overall wellbeing. Faecal microRNAs (miRNAs) offer valuable non-invasive insights into the transcriptional state of the intestine. However, typical faecal miRNA yields and profiles remain incompletely characterised. Here, we develop an optimised protocol for faecal miRNA detection, and describe a reproducible murine faecal miRNA profile across several studies by performing a meta-analysis. By examining faecal miRNA changes during chronic infection with the gastrointestinal helminth, Trichuris muris, we identify the altered expression of miRNAs associated with fibrosis, barrier integrity and wound healing. Fibrosis was confirmed in vivo, suggesting a role for these miRNAs in regulating wound healing during chronic infection where the production of classical wound healing Th2 cytokines are low. Further implementations of this technique can identify novel hypotheses and therapeutic strategies in diverse disease contexts.

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Trichuris muris transcriptomics

Project description:Trichuris muris is very closely related to the human parasite T. trichiura sharing cross reactive antigens. Moreover, it is a remarkably tractable model system for dissecting immune responses and host parasite relationships and is actively being investigated in a number of laboratories worldwide. T. muris is a naturally occurring nematode parasite of mice which resides in the caecum and colon and has a direct oral faecal life cycle. High-throughput sequencing of Trichuris muris transcriptome for de novo assembly of transcripts. The main objective of this project is to recognize genes expressed in given life stages. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

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Trichuris muris

Project description:Trichuris muris overview

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Extracellular vesicles Trichuris muris

Project description:We analysed the exosomes secreted by the nematode Trichuris muris. Two replicates of exosomes were analysed using a 5600+ mass spectrometer

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An optimised faecal microRNA sequencing pipeline reveals fibrosis in Trichuris muris infection.

Project description:The intestine is a site of diverse functions including digestion, nutrient absorption, immune surveillance, and microbial symbiosis. Intestinal microRNAs (miRNAs) are detectable in faeces and regulate barrier integrity, host-microbe interactions and the immune response, potentially offering valuable non-invasive tools to study intestinal health. However, current experimental methods are suboptimal and heterogeneity in study design limits the utility of faecal miRNA data. Here, we develop an optimised protocol for faecal miRNA detection and report a reproducible murine faecal miRNA profile in healthy mice. We use this pipeline to study faecal miRNAs during infection with the gastrointestinal helminth, Trichuris muris, revealing roles for miRNAs in fibrosis and wound healing. Intestinal fibrosis was confirmed in vivo using Hyperion® imaging mass cytometry, demonstrating the efficacy of this approach. Further applications of this optimised pipeline to study host-microbe interactions and intestinal disease will enable the generation of hypotheses and therapeutic strategies in diverse contexts.

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mRNA data from extracellular vesicles secreted by Trichuris muris

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Project description:We measured the gene expression differences in germinal centre B cells from day 13 Trichuris muris-infected mice in which MLL1 is conditionally deleted in mature B cells

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